The Northern Irishman leaves following four years on Wearside, helping the club rise from League One to the Premier League.
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The decision to split was made mutually, insist Sunderland.
Sporting Director Kristjaan Speakman said: “Stuart has made a significant contribution to Sunderland AFC throughout his time at the Club. His professionalism, expertise, and dedication have been evident throughout, and he has played a key part in our progress in recent years.
"He worked tirelessly through the summer to ensure continuity and consistency in our recruitment processes, and he leaves with our gratitude and best wishes for the future. Stuart will always be welcome back at the Stadium of Light.”